Graeme Lee’s side drifted in and out of proceedings before ultimately falling short against a side who may well be plying their trade in League One next season.
An early goal from Sam Hoskins was added to in the second half by Chanka Zimba with Lee’s side unable to find a breakthrough despite having several chances themselves throughout the afternoon.
It’s a result which will end any slight hopes of a play-off push this season with Pools now 12 points adrift and just eight games remaining having also slipped into the bottom half of the table.
And here are some of the key talking points and moments you might have missed from the defeat at Sixfields.
Early touch for Bilokapic
It was an eventful 24-hours for teenage goalkeeper Nicholas Bilokapic as the Huddersfield Town loanee made his Pools debut.
Bilokapic was called into action after No.1 Ben Killip went down with an illness the night before the trip to Northampton despite the teenager being on international duty with Australia less than 24 hours earlier.
The Terriers stopper caught an early flight back from the Netherlands to make his Pools debut and also caught an early touch of the ball.
Straight from the kick-off Pools were keen to give the 19-year-old a touch of the ball and unfortunately for him it was somewhat of a shanked clearance into touch.
But Bilokapic soon got to grips with the game as he made a big save in the opening minutes to deny Mitch Pinnock.
Bilokapic may have ended on the losing side during his debut but overall he gave a solid account of himself between the posts, something which will offer encouragement to both Lee and Pools supporters should he be required again between now and the end of the campaign.
It was a frustrating afternoon for Pools and Omar Bogle in particular as the striker failed to make an impact on the game.
And Bogle let his emotions boil over somewhat in the closing stages of the first half after a coming together with Louis Appere.
The Cobblers defender went down rather easily, much to Bogle’s disliking, and the Pools forward continued to vent his opinions to the referee until the half-time whistle perhaps saved him from a caution.
But his antics did not save him from becoming the pantomime villain for home fans who heckled the 29-year-old off the field to which he raised a wry smile and a thumbs up.
Jamie Sterry was left perplexed with Cobblers winger Beryly Lubala when the 24-year-old looked set to object to some good sportsmanship after an injury to Luke Molyneux.
Molyneux was sent tumbling to the floor by Fraser Horsfall and looked in some discomfort as he clutched his back.
Sterry, quick to notice his teammate’s concern, cleared the ball into touch so the Pools frontman could receive treatment.
But Molyneux soon returned to his feet as Lubala collected the ball and looked set to play on as usual from the throw-in to put the Cobblers on the attack.
Sterry was left bemused as he got set back in his fullback back position before Pinnock took charge of the situation and hurled the ball down the touchline back to Pools for a goalkick as common sense prevailed in the end.
A tale of set pieces
Pools headed into the game knowing what potentially was heading their way against a team who had scored almost half of their goals this season from set plays.
But despite having a number of freekicks and long throw-ins, Pools dealt relatively well with what the Cobblers threw at them for the most part.
In fact, it was Pools themselves who had more opportunities from set pieces with Lee’s side having eight corners to Northampton’s two.
But unfortunately for Pools, those routines did not come to any fruition and it was Jon Brady’s side who claimed their customary set piece goal in the second half after a mistake from Gary Liddle allowed Zimba to convert from close range.
It was encouraging that Pools had more opportunities to get the ball in the box but more must be done to capitalise on those openings.
“We needed a bit more determination in both boxes. That’s what’s cost us,” said Lee.
“We have not defended our box and even though we’ve created good chances there’s still opportunities when that ball is getting put in there that we’re not really fighting or scrapping for.
“It seems as though the Northampton players got their head on it or their foot on it and cleared balls and that affects games in a massive way.”
Pools fans should be used to it by now, but Saturday’s defeat continued their hoodoo at Sixfields.
Pools have now faced Northampton on their own patch 28 times without tasting victory since their most recent success at Sixfields coming in the old Division Four back on December, 20, 1969, losing 22 of those 28 meetings.
It’s the kind of record which makes you applaud the 320 travelling supporters even more when the outcome so often goes against Pools in this particular fixture.
“I wasn't aware of it, and the players won’t have been aware of it,” Lee told The Mail.
“Unfortunately it hasn't helped and we’ve backed that stat up again today.”
Play-off hopes extinguished
While still very much mathematically possible, defeat at Sixfields more than likely ends Pools’ faint hopes of reaching the play-offs.
With results elsewhere, Pools are now 12 points off seventh with just eight games remaining.
It was always going to be a big ask for Lee’s side to find a path towards the play-offs and they should not be deterred in not reaching them.
This remains an excellent return to the Football League for Pools who can now perhaps set their focus to climbing back into the top half of the table instead.